Integrated DNA and RNA extraction and purification on an automated microfluidic cassette from bacterial and viral pathogens causing community-acquired lower respiratory tract infections

Lab on a Chip ◽  
2014 ◽  
Vol 14 (9) ◽  
pp. 1519-1526 ◽  
Author(s):  
Liesbet Van Heirstraeten ◽  
Peter Spang ◽  
Carmen Schwind ◽  
Klaus S. Drese ◽  
Marion Ritzi-Lehnert ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Rna Extraction ◽  
Lower Respiratory Tract Infections ◽  
Viral Pathogens ◽  
Dna And Rna ◽  
Extraction And Purification ◽  
Tract Infections

Fully automated LOC can reproduce and outperform benchtop NA-sample preparation starting with swab samples.

scholarly journals An Overview of Antivirals for Treating Lower Respiratory Tract Infections

2021 ◽  
Vol 66 (1) ◽  
Author(s):  
Alicia Elvira Cruz Jiménez ◽  
Liliana Quintanar Vera ◽  
J. Armando Lujan-Montelongo
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
World Health ◽  
High Morbidity ◽  
Lower Respiratory Tract Infections ◽  
Viral Pathogens ◽  
El Sistema ◽  
Health Organization ◽  
Tract Infections

Abstract. Covid-19 has resulted in a worldwide epidemic (pandemic) with high morbidity and mortality, which has generated efforts in various areas of research looking for safe and effective treatments to combat the virus that generates this disease: SARS-CoV-2. However, several viruses have been emerged/adapted in the last few decades, also affecting the respiratory system. According to the world health organization (WHO), lower respiratory tract infections (LRTIs) are one of the leading causes of death worldwide, and viruses are playing important roles as the cause of these infections. In contrast to the vast repertoire of antibiotics that exist to treat bacteria-caused LRTIs, there are a very few antivirals approved for the treatment of virus-caused LRTIs, whose approach consists mainly of drug reuse. This minireview deals on the main viral pathogens that cause LRTIs and some of the most relevant antivirals to counter them (available drugs and molecules in research/clinical trials), with concise comments of their mechanism of action.   Resumen. Covid-19 ha resultado en una epidemia mundial (pandemia) con alta morbilidad y mortalidad, lo que ha generado esfuerzos en diversas áreas de investigación en la búsqueda de tratamientos seguros y eficaces para combatir el virus que genera esta enfermedad: el SARS-CoV-2. Sin embargo, un número de virus han surgido o se han adaptado en las últimas décadas, que también afectan el sistema respiratorio. Según la Organización Mundial de la Salud (OMS), las infecciones en vías respiratorias inferiores (LRTIs, por sus siglas en inglés) son una de las principales causas de muerte a nivel mundial, siendo los virus de los principales patógenos causantes de estas infecciones. En contraste con el repertorio amplio de antibióticos que existen para tratar LRTIs causadas por bacterias, existen muy pocos antivirales aprobados para su tratamiento, cuyo enfoque consiste principalmente en la reutilización de fármacos. Este ensayo consiste en una breve revisión de los principales agentes virales que causan LRTIs y de los antivirales más relevantes para combatir los virus que las causan (tanto fármacos disponibles como moléculas en fases de investigación o clínicas), con comentarios concisos sobre su mecanismo de acción.

scholarly journals Viral pathogens associated with acute lower respiratory tract infections in children younger than 5 years of age in Bulgaria

2018 ◽  
Vol 50 (1) ◽  
pp. 117-125 ◽  
Author(s):  
Neli Korsun ◽  
Svetla Angelova ◽  
Ivelina Trifonova ◽  
Irina Georgieva ◽  
Silvia Voleva ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Lower Respiratory Tract Infections ◽  
Viral Pathogens ◽  
Tract Infections

Clinical Utility of In-house Metagenomic Next-generation Sequencing for the Diagnosis of Lower Respiratory Tract Infections and Analysis of the Host Immune Response

2020 ◽  
Vol 71 (Supplement_4) ◽  
pp. S416-S426
Author(s):  
Hongbin Chen ◽  
Yuyao Yin ◽  
Hua Gao ◽  
Yifan Guo ◽  
Zhao Dong ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Respiratory Tract ◽  
Predictive Value ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Next Generation ◽  
Lower Respiratory Tract Infections ◽  
Dna And Rna ◽  
Tract Infections ◽  
Generation Sequencing

Abstract Background Only few pathogens that cause lower respiratory tract infections (LRTIs) can be identified due to limitations of traditional microbiological methods and the complexity of the oropharyngeal normal flora. Metagenomic next-generation sequencing (mNGS) has the potential to solve this problem. Methods This prospective observational study sequentially enrolled 93 patients with LRTI and 69 patients without LRTI who visited Peking University People’s Hospital in 2019. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA and RNA) and traditional microbiological assays. Human transcriptomes were compared between LRTI and non-LRTI, bacterial and viral LRTI, and tuberculosis and nontuberculosis groups. Results Among 93 patients with LRTI, 20%, 35%, and 65% of cases were detected as definite or probable pathogens by culture, all microbiological tests, and mNGS, respectively. Our in-house BALF mNGS platform had an approximately 2-working-day turnaround time and detected more viruses and fungi than the other methods. Taking the composite reference standard as a gold standard, it had a sensitivity of 66.7%, specificity of 75.4%, positive-predictive value of 78.5%, and negative-predictive value of 62.7%. LRTI-, viral LRTI–, and tuberculosis-related differentially expressed genes were respectively related to immunity responses to infection, viral transcription and response to interferon-γ pathways, and perforin 1 and T-cell receptor B variable 9. Conclusions Metagenomic DNA and RNA-seq can identify a wide range of LRTI pathogens, with improved sensitivity for viruses and fungi. Our in-host platform is likely feasible in the clinic. Host transcriptome data are expected to be useful for the diagnosis of LRTIs.

scholarly journals Clinical and Pathogenic Characteristics of Lower Respiratory Tract Infection Treated at the Vietnam National Children’s Hospital

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Hien T. Pham ◽  
Phuc T. T. Nguyen ◽  
Sinh T. Tran ◽  
Thuy T. B. Phung
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Patient Management ◽  
Respiratory Infections ◽  
Lower Respiratory Tract Infections ◽  
Viral Pathogens ◽  
Improve Patient Management ◽  
Tract Infections ◽  
Improve Patient

Lower respiratory tract infections are commonly caused by viruses and cause significant morbidity and mortality among children. Early identification of the pathological agent causing these infections is essential to avoid unnecessary antibiotic use and improve patient management. Multiplex PCR techniques were recently developed to detect multiple viral pathogens using a single PCR reaction. In this study, we identify viral pathogens in children with respiratory infections. We collected 194 nasopharyngeal aspirates from infants (2–24 months old) with lower respiratory tract infections treated at the Vietnam National Children’s Hospital between November 2014 and June 2015 and assessed the presence of 16 virus types and subtypes by multiplex PCR using the xTAG Respiratory Viral Panel (RVP) assay. Overall, 73.7% of the samples were positive for at least one virus, and 24.2% corresponded to infections with multiple viruses. The most common viruses were respiratory syncytial virus and enterovirus/rhinovirus. These viruses were more frequent among younger patients (2–5 months old) and caused symptoms similar to those of bronchiolitis and pneumonia. The most common clinical manifestation caused by respiratory tract infection was bronchiolitis. Elevated neutrophils levels were associated with adenovirus infection. Our results showed that the xTAG Respiratory Viral Panel (RVP) can effectively detect multiple viruses causing respiratory infections in children and that the nasopharyngeal aspirates are a good sample choice to detect respiratory viruses in children. Applying this approach in the clinical setting would improve patient management and allow early diagnosis, thus avoiding the unnecessary use of antibiotics.

scholarly journals A Prospective Study on Respiratory Viral Pathogens Causing Acute Lower Respiratory Infections in Children below Five Years of Ageat a Tertiary Care Hospital of India

2021 ◽  
Author(s):  
Apoorva T Raju ◽  
Rojaleen Das ◽  
Nikki Rai ◽  
Ajay Kumar ◽  
Rajni Gaind
Keyword(s):  
Respiratory Tract ◽  
Prospective Study ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Care Hospital ◽  
Age Group ◽  
Lower Respiratory Tract Infections ◽  
Viral Pathogens ◽  
Multiplex Qpcr ◽  
Tract Infections

Introduction: The lower respiratory tract infections are a major cause of mortality in children below five years of age. Majority of the time the infection is self-limiting but often gets severe and fatal depending on various factors like age, aetiology, time of diagnosis, appropriate treatment, etc. Aim: To study viral aetiology of Acute Lower Respiratory tract Infections (ALRI) using multiplex real time qualitative Polymerase Chain Reactions (qPCR) among hospitalised children under five years of age. Materials and Methods: This was a hospital based prospective study conducted over a period of two years from June 2015 to May 2017, a throat and nasal swab was collected from 512 children ≤5 years who were being hospitalised for ALRI. The samples were tested by multiplex qPCR to detect viral and p<0.05 was considered as statistically significant. Results: Out of 512 cases, 317 children were further studied. It was found that highest number of ALRI were observed in children of age less than six months i.e., 38.9% followed by 29.4%, 14.8% and 16.9% in the age group of 6-12 months, 12-24 months and 24-60 months, respectively. The one/more viral pathogens were detected in 58.3% (185/317) children. Respiratory Synctial Virus (RSV) was most common virus detected in 51.9% followed by Human Rhinovirus (HRV) in 23.2%. RSV was found to be statistically significant in infants and causes very severe ALRI. Conclusion: The use of multiplex qPCR has clarified the scenario of different respiratory viral aetiologies causing ALRI in different age group of children. The study results enhance knowledge for making strategy to prevent severity of ALRI in different age group, seasons and geographical area.

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